Contacts of the helix formed by residues 448 - 458 (chain B) in PDB entry 4PKO
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLU 448 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420B ILE* 4.0 28.2 - - + +
423B ALA* 5.6 1.8 - - + -
444B LEU 4.0 12.8 - - - +
445B ARG* 3.6 19.0 - - - +
446B ALA 3.1 0.2 - - - -
447B MET* 1.3 80.1 - - - +
449B ALA* 1.3 64.2 + - - +
450B PRO 3.4 0.2 - - - -
451B LEU* 3.2 14.4 + - - +
452B ARG* 2.9 50.7 + - - +
466B ALA* 5.1 0.4 - - + +
470B LYS* 3.2 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 449 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B VAL* 3.8 15.7 - - + +
98B ALA* 3.7 22.4 - - + -
445B ARG 4.2 1.6 + - - +
446B ALA* 3.1 18.4 + - - +
448B GLU* 1.3 76.9 - - - +
450B PRO* 1.3 67.5 - - + +
452B ARG* 3.2 13.9 - - - +
453B GLN* 2.9 27.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 450 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.7 5.8 - - + +
91B THR* 4.3 16.4 - - + +
94B VAL* 4.0 13.2 - - + -
95B LEU* 3.3 27.6 - - + -
415B GLY 5.3 0.2 - - - -
416B GLY* 4.8 7.4 - - - -
419B LEU* 3.9 20.9 - - + -
446B ALA 3.5 5.6 - - - +
447B MET 3.4 13.2 - - - +
448B GLU 3.4 0.2 - - - -
449B ALA* 1.3 97.0 - - + +
451B LEU* 1.3 61.2 + - - +
453B GLN* 3.4 3.0 + - + +
454B ILE* 3.1 29.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
415B GLY* 3.2 28.7 - - - +
416B GLY* 4.5 7.6 - - - +
417B VAL* 4.3 13.7 - - + +
420B ILE* 4.8 11.9 - - + -
447B MET 5.1 0.8 + - - +
448B GLU* 3.2 8.4 + - - +
450B PRO* 1.3 79.9 - - - +
452B ARG* 1.3 69.1 + - + +
454B ILE* 3.2 16.4 + - + +
455B VAL* 3.2 15.5 + - + +
465B VAL* 4.1 17.3 - - + +
466B ALA* 4.0 29.2 - - + +
469B VAL* 4.1 26.2 - - + -
478B TYR* 5.2 8.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 452 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B ARG 5.6 0.9 + - - -
448B GLU* 2.9 53.1 + - - +
449B ALA* 3.2 16.4 - - - +
451B LEU* 1.3 82.9 - - + +
453B GLN* 1.3 56.5 + - - +
455B VAL* 3.9 1.7 - - - +
456B LEU* 3.1 26.6 + - - +
462B PRO* 3.3 34.8 - - + +
463B SER* 4.6 16.1 + - - +
466B ALA* 3.6 22.4 - - + +
467B ASN* 5.7 1.0 + - - -
470B LYS* 4.7 4.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 453 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 3.4 51.5 - - + +
31B LEU* 3.7 11.5 - - + +
94B VAL* 4.0 18.8 - - + -
449B ALA* 2.9 19.6 + - + +
450B PRO 3.5 5.6 - - - +
451B LEU 3.1 0.2 - - - -
452B ARG* 1.3 76.5 - - - +
454B ILE* 1.3 64.1 + - - +
456B LEU* 3.2 26.1 + - - +
457B ASN* 3.0 36.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 454 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU* 3.6 22.7 - - + -
32B GLY* 4.2 7.0 - - - -
33B PRO* 4.1 15.5 - - + -
415B GLY* 4.2 32.1 - - - +
416B GLY* 4.8 1.1 - - - +
450B PRO* 3.1 18.2 - - + +
451B LEU* 3.2 7.3 + - + +
453B GLN* 1.3 77.6 - - - +
455B VAL* 1.3 61.7 + - + +
457B ASN* 3.2 24.0 + - - +
458B CYS* 3.4 10.2 + - - -
478B TYR* 6.2 0.7 - - + -
480B ALA* 4.0 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B LEU* 3.2 17.6 + - + +
452B ARG* 3.9 7.4 - - - +
454B ILE* 1.3 75.7 - - + +
456B LEU* 1.3 62.5 + - - +
458B CYS* 2.9 29.5 + - - +
460B GLU* 3.3 32.9 + - + +
461B GLU 3.8 6.7 - - - +
462B PRO* 4.0 5.4 - - + -
465B VAL* 3.6 49.1 - - + -
478B TYR* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 456 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS* 5.8 0.4 - - - +
452B ARG 3.1 18.4 + - - +
453B GLN* 3.2 29.8 + - - +
455B VAL* 1.3 76.1 - - - +
457B ASN* 1.3 58.9 + - - +
459B GLY* 2.8 22.8 + - - -
460B GLU 3.8 12.8 - - - +
462B PRO* 3.9 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 457 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LYS 3.4 21.3 + - - +
29B VAL* 4.2 11.0 - - - +
31B LEU* 2.8 35.1 + - - +
34B LYS* 3.6 15.7 - - + +
35B GLY* 4.3 14.8 - - - +
36B ARG* 4.8 13.0 + - + +
453B GLN* 3.0 27.8 + - - +
454B ILE* 3.4 9.6 - - - +
455B VAL 3.1 0.4 - - - -
456B LEU* 1.3 76.6 - - - +
458B CYS* 1.3 59.1 + - - +
459B GLY 3.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 458 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS* 3.5 42.5 + - + +
36B ARG* 6.3 0.2 - - - -
454B ILE* 3.5 14.6 - - - -
455B VAL* 2.9 14.6 + - + +
457B ASN* 1.3 77.3 - - - +
459B GLY* 1.3 60.4 + - - +
460B GLU* 3.7 23.2 - - + +
478B TYR* 5.0 4.3 - - - -
480B ALA* 3.9 25.8 - - - -
483B GLU* 4.6 4.7 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il